Gene Prediction: the End of the Beginning Comment Colin Semple
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Applied Category Theory for Genomics – an Initiative
Applied Category Theory for Genomics { An Initiative Yanying Wu1,2 1Centre for Neural Circuits and Behaviour, University of Oxford, UK 2Department of Physiology, Anatomy and Genetics, University of Oxford, UK 06 Sept, 2020 Abstract The ultimate secret of all lives on earth is hidden in their genomes { a totality of DNA sequences. We currently know the whole genome sequence of many organisms, while our understanding of the genome architecture on a systematic level remains rudimentary. Applied category theory opens a promising way to integrate the humongous amount of heterogeneous informations in genomics, to advance our knowledge regarding genome organization, and to provide us with a deep and holistic view of our own genomes. In this work we explain why applied category theory carries such a hope, and we move on to show how it could actually do so, albeit in baby steps. The manuscript intends to be readable to both mathematicians and biologists, therefore no prior knowledge is required from either side. arXiv:2009.02822v1 [q-bio.GN] 6 Sep 2020 1 Introduction DNA, the genetic material of all living beings on this planet, holds the secret of life. The complete set of DNA sequences in an organism constitutes its genome { the blueprint and instruction manual of that organism, be it a human or fly [1]. Therefore, genomics, which studies the contents and meaning of genomes, has been standing in the central stage of scientific research since its birth. The twentieth century witnessed three milestones of genomics research [1]. It began with the discovery of Mendel's laws of inheritance [2], sparked a climax in the middle with the reveal of DNA double helix structure [3], and ended with the accomplishment of a first draft of complete human genome sequences [4]. -
The EMBL-European Bioinformatics Institute the Hub for Bioinformatics in Europe
The EMBL-European Bioinformatics Institute The hub for bioinformatics in Europe Blaise T.F. Alako, PhD [email protected] www.ebi.ac.uk What is EMBL-EBI? • Part of the European Molecular Biology Laboratory • International, non-profit research institute • Europe’s hub for biological data, services and research The European Molecular Biology Laboratory Heidelberg Hamburg Hinxton, Cambridge Basic research Structural biology Bioinformatics Administration Grenoble Monterotondo, Rome EMBO EMBL staff: 1500 people Structural biology Mouse biology >60 nationalities EMBL member states Austria, Belgium, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom Associate member state: Australia Who we are ~500 members of staff ~400 work in services & support >53 nationalities ~120 focus on basic research EMBL-EBI’s mission • Provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress • Contribute to the advancement of biology through basic investigator-driven research in bioinformatics • Provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators • Help disseminate cutting-edge technologies to industry • Coordinate biological data provision throughout Europe Services Data and tools for molecular life science www.ebi.ac.uk/services Browse our services 9 What services do we provide? Labs around the -
Functional Effects Detailed Research Plan
GeCIP Detailed Research Plan Form Background The Genomics England Clinical Interpretation Partnership (GeCIP) brings together researchers, clinicians and trainees from both academia and the NHS to analyse, refine and make new discoveries from the data from the 100,000 Genomes Project. The aims of the partnerships are: 1. To optimise: • clinical data and sample collection • clinical reporting • data validation and interpretation. 2. To improve understanding of the implications of genomic findings and improve the accuracy and reliability of information fed back to patients. To add to knowledge of the genetic basis of disease. 3. To provide a sustainable thriving training environment. The initial wave of GeCIP domains was announced in June 2015 following a first round of applications in January 2015. On the 18th June 2015 we invited the inaugurated GeCIP domains to develop more detailed research plans working closely with Genomics England. These will be used to ensure that the plans are complimentary and add real value across the GeCIP portfolio and address the aims and objectives of the 100,000 Genomes Project. They will be shared with the MRC, Wellcome Trust, NIHR and Cancer Research UK as existing members of the GeCIP Board to give advance warning and manage funding requests to maximise the funds available to each domain. However, formal applications will then be required to be submitted to individual funders. They will allow Genomics England to plan shared core analyses and the required research and computing infrastructure to support the proposed research. They will also form the basis of assessment by the Project’s Access Review Committee, to permit access to data. -
Meeting Review: Bioinformatics and Medicine – from Molecules To
Comparative and Functional Genomics Comp Funct Genom 2002; 3: 270–276. Published online 9 May 2002 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.178 Feature Meeting Review: Bioinformatics And Medicine – From molecules to humans, virtual and real Hinxton Hall Conference Centre, Genome Campus, Hinxton, Cambridge, UK – April 5th–7th Roslin Russell* MRC UK HGMP Resource Centre, Genome Campus, Hinxton, Cambridge CB10 1SB, UK *Correspondence to: Abstract MRC UK HGMP Resource Centre, Genome Campus, The Industrialization Workshop Series aims to promote and discuss integration, automa- Hinxton, Cambridge CB10 1SB, tion, simulation, quality, availability and standards in the high-throughput life sciences. UK. The main issues addressed being the transformation of bioinformatics and bioinformatics- based drug design into a robust discipline in industry, the government, research institutes and academia. The latest workshop emphasized the influence of the post-genomic era on medicine and healthcare with reference to advanced biological systems modeling and simulation, protein structure research, protein-protein interactions, metabolism and physiology. Speakers included Michael Ashburner, Kenneth Buetow, Francois Cambien, Cyrus Chothia, Jean Garnier, Francois Iris, Matthias Mann, Maya Natarajan, Peter Murray-Rust, Richard Mushlin, Barry Robson, David Rubin, Kosta Steliou, John Todd, Janet Thornton, Pim van der Eijk, Michael Vieth and Richard Ward. Copyright # 2002 John Wiley & Sons, Ltd. Received: 22 April 2002 Keywords: bioinformatics; -
Life Will Never Be the Same Annual Genome Sequencing and Biology Meeting, Cold Spring Harbor Laboratory, USA
Yeast Yeast 2000; 17: 241±243. Meeting Review Life will never be the same Annual Genome Sequencing and Biology Meeting, Cold Spring Harbor Laboratory, USA. May 2000 M.A. Strivens* MRC Mammalian Genetics Unit and UK Mouse Genome Centre, Harwell, UK *Correspondence to: M. A. Strivens, MRC Mammalian Genetics Unit and UK Mouse Genome Centre, Harwell, Oxfordshire OX11 0RD,UK. E-mail: [email protected] It seems appropriate that the Cold Spring Harbor The crux of the whole-genome shotgun strategy is Genome Sequencing and Biology Meeting, which the assembly technique. Gene Myers (Celera Geno- witnessed the creation of the Human Genome mics) reported on how the `double-barrelled' shot- Organization (HUGO) in 1988, should this year gun2 approach had given a signi®cant advantage to present three major advances in genomic science: the computer algorithms employed in the assembly the completion of the ®nished sequence of Droso- of the ¯y genome. The assembly system employs a phila melanogaster; the announcement that 85% of bottom-up, nucleating strategy, initially assembling the genome of Homo sapiens is now in draft small islands of sequence of high con®dence sequence; and the complete, ®nished sequence of a (diverting the assembly of repeat regions to later second human chromosome, chromosome 21. Other stages) and then searching for other sequence major sessions of the meeting focused on single (including orientation data from clone end- nucleotide polymorphisms (SNPs), ethical, legal and sequencing) to join the islands together. In addition, social implications (ELSI), as well as comparative he con®rmed a less than 0.5% error rate in the and functional genomics. -
Reconstructing Contiguous Regions of an Ancestral Genome
Downloaded from www.genome.org on December 5, 2006 Reconstructing contiguous regions of an ancestral genome Jian Ma, Louxin Zhang, Bernard B. Suh, Brian J. Raney, Richard C. Burhans, W. James Kent, Mathieu Blanchette, David Haussler and Webb Miller Genome Res. 2006 16: 1557-1565; originally published online Sep 18, 2006; Access the most recent version at doi:10.1101/gr.5383506 Supplementary "Supplemental Research Data" data http://www.genome.org/cgi/content/full/gr.5383506/DC1 References This article cites 20 articles, 11 of which can be accessed free at: http://www.genome.org/cgi/content/full/16/12/1557#References Open Access Freely available online through the Genome Research Open Access option. Email alerting Receive free email alerts when new articles cite this article - sign up in the box at the service top right corner of the article or click here Notes To subscribe to Genome Research go to: http://www.genome.org/subscriptions/ © 2006 Cold Spring Harbor Laboratory Press Downloaded from www.genome.org on December 5, 2006 Methods Reconstructing contiguous regions of an ancestral genome Jian Ma,1,5,6 Louxin Zhang,2 Bernard B. Suh,3 Brian J. Raney,3 Richard C. Burhans,1 W. James Kent,3 Mathieu Blanchette,4 David Haussler,3 and Webb Miller1 1Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA; 2Department of Mathematics, National University of Singapore, Singapore 117543; 3Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA; 4School of Computer Science, McGill University, Montreal, Quebec H3A 2B4, Canada This article analyzes mammalian genome rearrangements at higher resolution than has been published to date. -
Download Final Programme
Session Overview Saturday 17 September 2011 11:15 - 13:15 Arrival and Registration ATC Main Entrance 13:15 - 13:30 Welcome and Opening Remarks Klaus Tschira Auditorium 13:30 - 18:00 Session 1: Somatic Genetics I Chaired by David Tuveson and Ewan Birney Klaus Tschira Auditorium 18:00 - 19:00 Keynote Lecture: Lynda Chin Klaus Tschira Auditorium 19:00 - 20:30 Dinner ATC Canteen Sunday 18 September 2011 09:00 - 12:30 Session 2: Somatic Genetics II / Epigenetics Chaired by James R. Downing Klaus Tschira Auditorium 12:30 - 14:30 Poster Session I and Lunch ATC Foyer and Helix A 14:30 - 18:30 Session 3: Mouse Genetics Chaired by Lynda Chin Klaus Tschira Auditorium 18:30 - 23:00 Gala Dinner and Live Music ATC Canteen and ATC Rooftop Lounge Page 1 EMBO|EMBL Symposium: Cancer Genomics Monday 19 September 2011 09:00 - 13:00 Session 4: Computational Chaired by Peter Lichter Klaus Tschira Auditorium 13:00 - 15:00 Poster Session II and Lunch ATC Foyer and Helix A 15:00 - 16:00 Session 5: Somatic Genetics III Chaired by Andy Futreal Klaus Tschira Auditorium 16:00 - 17:00 Keynote Lecture: Michael Stratton Klaus Tschira Auditorium 17:00 - 17:15 Closing Remarks and Poster Prize Klaus Tschira Auditorium Page 2 Programme Saturday 17 September 2011 11:15 - 13:15 Arrival and Registration ATC Main Entrance 13:15 - 13:30 Welcome and Opening Remarks Klaus Tschira Auditorium 13:30 - 18:00 Session 1: Somatic Genetics I Chaired by David Tuveson and Ewan Birney Klaus Tschira Auditorium 13:30 - 14:00 Somatic genomic alterations in chronic lymphocytic 1 leukemia Elias -
The Ethos and Effects of Data-Sharing Rules: Examining The
Informed consent for: "The ethos and effects of data-sharing rules: Examining the history of the 'Bermuda principles' and their effects on 21 st century science" University of Adelaide Duke University Researchers at the University of Adelaide, Australia, and the IGSP Center for Genome Ethics, Law & Policy, Duke University, are engaged in research on the Bermuda Principles for sharing DNA sequence data from high-volume sequencing centers. You have been selected for an interview because we believe that the recollections you may have of your experiences with the International Strategy Meetings for Human Genome Sequencing (1996-1998) will be interesting and helpful for our project. We expect that interviews will last from 30 minutes to much longer, but you may stop your interview at any time. Your participation is strictly voluntary, and you do not have to answer every question asked. Your interview is being recorded and we may take written notes during the interview. After your interview, we may prepare a typed transcript of the interview. If we prepare a transcript, you will have an opportunity to review it and to make deletions and corrections. Unless you indicate otherwise, the information that you provide in this interview will be "on the record"-that is, it can be attributed to you in the various articles and chapters that we plan to write, and thus could become public through these channels. Jf, however, at some point in the interview you want to provide us with information that might be useful for us to know, but which you do not want to have attributed to you, you should tell us that you wish to go "off the record" and we will stop the recording. -
Duplication, Deletion, and Rearrangement in the Mouse and Human Genomes
Evolution’s cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes W. James Kent*†, Robert Baertsch*, Angie Hinrichs*, Webb Miller‡, and David Haussler§ *Center for Biomolecular Science and Engineering and §Howard Hughes Medical Institute, Department of Computer Science, University of California, Santa Cruz, CA 95064; and ‡Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802 Edited by Michael S. Waterman, University of Southern California, Los Angeles, CA, and approved July 11, 2003 (received for review April 9, 2003) This study examines genomic duplications, deletions, and rear- depending on details of definition and method. The length rangements that have happened at scales ranging from a single distribution of synteny blocks was found to be consistent with the base to complete chromosomes by comparing the mouse and theory of random breakage introduced by Nadeau and Taylor (8, human genomes. From whole-genome sequence alignments, 344 9) before significant gene order data became available. In recent large (>100-kb) blocks of conserved synteny are evident, but these comparisons of the human and mouse genomes, rearrangements are further fragmented by smaller-scale evolutionary events. Ex- of Ն100,000 bases were studied by comparing 558,000 highly cluding transposon insertions, on average in each megabase of conserved short sequence alignments (average length 340 bp) genomic alignment we observe two inversions, 17 duplications within 300-kb windows. An estimated 217 blocks of conserved (five tandem or nearly tandem), seven transpositions, and 200 synteny were found, formed from 342 conserved segments, with deletions of 100 bases or more. This includes 160 inversions and 75 length distribution roughly consistent with the random breakage duplications or transpositions of length >100 kb. -
Contcenter for Genomic Regul
CONTCENTER FOR GENOMIC REGUL CRG SCIENTIFIC STRUCTURE . 4 CRG MANAGEMENT STRUCTURE . 6 CRG SCIENTIFIC ADVISORY BOARD (SAB) . 8 CRG BUSINESS BOARD . 9 YEAR RETROSPECT BY THE DIRECTOR OF THE CRG: MIGUEL BEATO . 10 GENE REGULATION. 14 p Chromatin and gene expression .....................16 p Transcriptional regulation and chromatin remodelling .....19 p Regulation of alternative pre-mRNA splicing during cell . 22 differentiation, development and disease p RNA interference and chromatin regulation . 26 p RNA-protein interactions and regulation . 30 p Regulation of protein synthesis in eukaryotes . 33 p Translational control of gene expression . 36 DIFFERENTIATION AND CANCER ...........................40 p Hematopoietic differentiation and stem cell biology..........42 p Myogenesis.....................................46 p Epigenetics events in cancer.......................49 p Epithelial homeostasis and cancer ...................52 ENTSATION ANNUAL REPORT 2006 GENES AND DISEASE .................................56 p Genetic causes of disease .............................58 p Gene therapy ......................................63 p Murine models of disease .............................66 p Neurobehavioral phenotyping of mouse models of disease .....68 p Gene function ......................................73 p Associated Core Facility: Genotyping Unit..................76 BIOINFORMATICS AND GENOMICS ..........................80 p Bioinformatics and genomics ...........................82 p Genomic analysis of development and disease ..............86 -
Concepts, Historical Milestones and the Central Place of Bioinformatics in Modern Biology: a European Perspective
1 Concepts, Historical Milestones and the Central Place of Bioinformatics in Modern Biology: A European Perspective Attwood, T.K.1, Gisel, A.2, Eriksson, N-E.3 and Bongcam-Rudloff, E.4 1Faculty of Life Sciences & School of Computer Science, University of Manchester 2Institute for Biomedical Technologies, CNR 3Uppsala Biomedical Centre (BMC), University of Uppsala 4Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences 1UK 2Italy 3,4Sweden 1. Introduction The origins of bioinformatics, both as a term and as a discipline, are difficult to pinpoint. The expression was used as early as 1977 by Dutch theoretical biologist Paulien Hogeweg when she described her main field of research as bioinformatics, and established a bioinformatics group at the University of Utrecht (Hogeweg, 1978; Hogeweg & Hesper, 1978). Nevertheless, the term had little traction in the community for at least another decade. In Europe, the turning point seems to have been circa 1990, with the planning of the “Bioinformatics in the 90s” conference, which was held in Maastricht in 1991. At this time, the National Center for Biotechnology Information (NCBI) had been newly established in the United States of America (USA) (Benson et al., 1990). Despite this, there was still a sense that the nation lacked a “long-term biology ‘informatics’ strategy”, particularly regarding postdoctoral interdisciplinary training in computer science and molecular biology (Smith, 1990). Interestingly, Smith spoke here of ‘biology informatics’, not bioinformatics; and the NCBI was a ‘center for biotechnology information’, not a bioinformatics centre. The discipline itself ultimately grew organically from the needs of researchers to access and analyse (primarily biomedical) data, which appeared to be accumulating at alarming rates simultaneously in different parts of the world. -
BIOINFORMATICS ISCB NEWS Doi:10.1093/Bioinformatics/Btp280
Vol. 25 no. 12 2009, pages 1570–1573 BIOINFORMATICS ISCB NEWS doi:10.1093/bioinformatics/btp280 ISMB/ECCB 2009 Stockholm Marie-France Sagot1, B.J. Morrison McKay2,∗ and Gene Myers3 1INRIA Grenoble Rhône-Alpes and University of Lyon 1, Lyon, France, 2International Society for Computational Biology, University of California San Diego, La Jolla, CA and 3Howard Hughes Medical Institute Janelia Farm Research Campus, Ashburn, Virginia, USA ABSTRACT Computational Biology (http://www.iscb.org) was formed to take The International Society for Computational Biology (ISCB; over the organization, maintain the institutional memory of ISMB http://www.iscb.org) presents the Seventeenth Annual International and expand the informational resources available to members of the Conference on Intelligent Systems for Molecular Biology bioinformatics community. The launch of ECCB (http://bioinf.mpi- (ISMB), organized jointly with the Eighth Annual European inf.mpg.de/conferences/eccb/eccb.htm) 8 years ago provided for a Conference on Computational Biology (ECCB; http://bioinf.mpi- focus on European research activities in years when ISMB is held inf.mpg.de/conferences/eccb/eccb.htm), in Stockholm, Sweden, outside of Europe, and a partnership of conference organizing efforts 27 June to 2 July 2009. The organizers are putting the finishing for the presentation of a single international event when the ISMB touches on the year’s premier computational biology conference, meeting takes place in Europe every other year. with an expected attendance of 1400 computer scientists, The multidisciplinary field of bioinformatics/computational mathematicians, statisticians, biologists and scientists from biology has matured since gaining widespread recognition in the other disciplines related to and reliant on this multi-disciplinary early days of genomics research.